Individuals differ in the exact nucleotide sequence of their genomes. These differences can be utilized to track the inheritance of chromosomal regions, allowing mutations produced by genetic screens or disease-causing gene alleles to be rapidly mapped. Approaches for identifying these changes, called single nucleotide polymorphisms or SNPs are rapidly improving, and yet both the discovery and genotyping of SNPs in all organisms, but particularly ones without known genome sequences, remains a major undertaking. The long-term objectives of this application are to develop techniques for SNP discovery and genotyping that are inexpensive, high-throughput, and are applicable to a variety of organisms. As sequence information becomes inexpensive and custom high-density tiling microarrays become readily available, Restriction site Associated DNA (RAD) tags provide superior characteristics for genotyping. Thousands of RAD tag markers are assayable with a single hybridization, the polymorphism is converted into a simple binary presence or absence of a DNA fragment several hundred nucleotides long, and the marker allows the rapid genotyping of large populations on a marker by marker basis, speeding fine-scale mapping. The specific aims are to 1) Optimize protocols for the discovery of RAD markers on tiling arrays and characterizing the design parameters of RAD markers when genetic mapping with pooled populations. 2) Develop methods for the high-throughput isolation of RAD tags, which will allow the genotyping of many individuals in a population. The RAD marker approach allows inexpensive, high- throughput screening of high-density genetic markers in any organism, a significant benefit for researchers wishing to understand the genetic basis of phenotype.Project narrative Identifying the genetic changes that cause disease in humans, or affect a biological process in a model organism, has been difficult. This application develops methods to allow genetic changes to be rapidly and inexpensively mapped to a small region of the genome.